Effect of C–H⋯S and C–H⋯Cl interactions on the conformational preference of inhibitors of TIBO family

Stabilizing Effect of a 4c/6e Hypervalent Bond in Dinitrodiphenyl Disulfides and Their Thermochemical Properties: Experimental and Computational Approach

Thermochemical properties and intramolecular interactions of 2,2'-dinitrodiphenyl disulfide (2DNDPDS) and 4,4'-dinitrodiphenyl disulfide (4DNDPDS) were determined and analyzed. Their standard molar formation enthalpies in the gas phase (ΔfHm°(g)'s) were experimentally determined; theoretically, they were computed using the G4 composite method and atomization reactions. Specifically, ΔfHm°(g)'s were obtained by combining formation enthalpies in the condensed phase and enthalpies of phase change. Formation enthalpies in the condensed phase were determined experimentally through combustion energies, which in turn were found by means of a rotatory bomb combustion calorimeter. Sublimation enthalpies were derived from thermogravimetric experiments, measuring the rate of mass loss and using Langmuir and Clausius-Clapeyron equations. Fusion enthalpies and heat capacities of the solid and liquid phases were measured as functions of temperature by differential scanning calorimetry, and the heat capacities of the gas phase were calculated via molecular orbital calculations. Theoretical and experimental ΔfHm°(g)'s differed by <5.5kJ·mol-1, and isomerization enthalpies are discussed. In addition, using theoretical tools [natural bond orbitals (NBO) and quantum theory of atoms in molecules (QTAIM)], intramolecular interactions were analyzed. An uncommon hypervalent four-center six-electron interaction of type O···S-S···O was found in 2DNDPDS. This hypervalent interaction, in addition to the extent of conjugation between the aryl and NO2 moieties and the formation of intramolecular C-H···S hydrogen bonds, counteracts the repulsion caused by steric repulsions. Hydrogen bonding was confirmed through geometric parameters as well as QTAIM.

Participation of S and Se in hydrogen and chalcogen bonds

The heavier chalcogen atoms S, Se, and Te can each participate in a range of different noncovalent interactions. They can serve as both proton donor and acceptor in H-bonds. Each atom can also act as electron acceptor in a chalcogen bond.

Evaluation of N-H...S and N-H...π interactions in O,O'-diethyl N-(2,4,6-trimethylphenyl)thiophosphate: a combination of X-ray crystallographic and theoretical studies

In the crystal structure of O,O'-diethyl N-(2,4,6-trimethylphenyl)thiophosphate, C₁₃H₂₂NO₂PS, two symmetrically independent thiophosphoramide molecules are linked through N-H...S and N-H...π hydrogen bonds to form a noncentrosymmetric dimer, with Z' = 2. The strengths of the hydrogen bonds were evaluated using density functional theory (DFT) at the M06-2X level within the 6-311++G(d,p) basis set, and by considering the quantum theory of atoms in molecules (QTAIM). It was found that the N-H...S hydrogen bond is slightly stronger than the N-H...π hydrogen bond. This is reflected in differences between the calculated N-H stretching frequencies of the isolated molecules and the frequencies of the same N-H units involved in the different hydrogen bonds of the hydrogen-bonded dimer. For these hydrogen bonds, the corresponding charge transfers, i.e. lp (or π)→σ*, were studied, according to the second-order perturbation theory in natural bond orbital (NBO) methodology. Hirshfeld surface analysis was applied for a detailed investigation of all the contacts participating in the crystal packing.

Structural flexibility of the sulfur mustard molecule at finite temperature from Car-Parrinello molecular dynamics simulations

Sulfur mustard (SM) is one of the most dangerous chemical compounds used against humans, mostly at war conditions but also in terrorist attacks. Even though the sulfur mustard has been synthesized over a hundred years ago, some of its molecular properties are not yet resolved. We investigate the structural flexibility of the SM molecule in the gas phase by Car-Parrinello molecular dynamics simulations. Thorough conformation analysis of 81 different SM configurations using density functional theory is performed to analyze the behavior of the system at finite temperature. The conformational diversity is analyzed with respect to the formation of intramolecular blue-shifting CH⋯S and CH⋯Cl hydrogen bonds. Molecular dynamics simulations indicate that all structural rearrangements between SM local minima are realized either in direct or non-direct way, including the intermediate structure in the last case. We study the lifetime of the SM conformers and perform the population analysis. Additionally, we provide the anharmonic dynamical finite temperature IR spectrum from the Fourier Transform of the dipole moment autocorrelation function to mimic the missing experimental IR spectrum.

Crystal structures, spectroscopic and theoretical study of novel Schiff bases of 2-(methylthiomethyl)anilines

New Schiff bases derived from p-methoxysalicylaldehyde and 2-(methylthiomethyl)anilines (substituted with methyl, methoxy, nitro) were synthesized and characterized by elemental analyses, FT-IR, NMR, electronic spectra and quantum chemical calculations. X-ray crystallography of two compounds showed the solid structures are stabilized by intramolecular and intermolecular H-bonds. The effect of OH⋯N interaction between the phenolic hydrogen and imine nitrogen on the proton and carbon NMR shifts, and the role of CH⋯O and CH⋯S contacts are discussed. The bond lengths and angles, (1)H and (13)C NMR data, E(LUMO-HOMO), dipole moments and polarizability of the compounds were predicted by density functional theory, DFT (B3LYP/6-31G∗∗) method. The experimental geometric parameters and the NMR shifts were compared with the calculated values, which gave good correlations. The electronic effects of aryl ring substituents (methyl, methoxy and nitro) on the properties of the resulting compounds, such as the color, NMR shifts, electronic spectra and the calculated energy band gaps, dipole moments and polarizability are discussed. Increase in electron density shifted the phenolic proton resonance to lower fields. The methoxy-substituted compound has a small dipole moment and subsequent large polarizability value. Highest polarity was indicated by the nitro compound which also showed high polarizability due to its larger size. The energy gaps obtained from E(LUMO-HOMO) calculations suggest these compounds may have applications as organic semiconducting materials.

A study of van der Waals complexes of 1,2-dichloroethane in paraffin oil by FTIR spectroscopy and ab initio calculations

Weak molecular interactions of 1,2-dichloroethane dissolved in paraffin oil were investigated by FTIR spectroscopy. Occurrence of isosbestic points in the spectra along with the factor analysis showed that DCE⋯DCE dimers are formed in solutions at DCE concentrations between 7 and 15 vol.%. It was found that both trans and gauche conformers are involved in the complexation, forming a tg-dimer. From the spectra collected at 200-222 K, the complexation enthalpy was determined: -4.2±0.4 kcal mol(-1). The equilibrium geometry of tg-dimer and the vibrational frequencies were determined from the density functional calculations performed at B3LYP/6-311++G(d,p) and 6-31G(d,p) levels. The C-C bonds of the two molecules involved in tg-dimers were found to be oriented nearly perpendicular to each other. The complexation energy calculated using 6-31G(d,p) and 6-311++G(d,p) basis sets was found to be -1.59 and -1.52 kcal mol(-1), respectively.

Weak H-bonds. Comparisons of CH···O to NH···O in proteins and PH···N to direct P···N interactions

Whereas CH···O H-bonds are usually weaker than interpeptide NH···O H-bonds, this is not necessarily the case within proteins. The nominally weaker CH···O are surprisingly strong, comparable to, and in some cases stronger than, the NH···O H-bonds in the context of the forces that hold together the adjacent strands in protein β-sheets. The peptide NH is greatly weakened as proton donor in certain conformations of the protein backbone, particularly extended structures, and forms correspondingly weaker H-bonds. The PH group is a weak proton donor, but will form PH···N H-bonds. However, there is a stronger interaction in which P can engage, in which the P atom, not the H, directly approaches the N electron donor to establish a direct P···N interaction. This approach is stabilized by the same sort of electron transfer from the N lone pair to the P-H σ* antibond that characterizes the PH···N H-bond.

Experimental and Theoretical Electron Density Study of a Highly Twisted Polycyclic Aromatic Hydrocarbon: 4-Methyl-[4]helicene

Helicenes are molecules of considerable interest in view of their aromaticity which persists despite a marked departure from planarity and because of the extreme potency of some of their metabolites as tumor and mutation promoters. In this study, the electron density of 4-methyl-[4]helicene (or 4-methylbenzo[c]phenanthrene) is studied topologically with an emphasis on the fjord region since this region is where metabolic activation is initiated. The molecule consists of four fused aromatic rings that assume a twisted geometry. This geometry brings two hydrogen atoms into close proximity in the fjord region of the molecule accompanied by the appearance of an intramolecular C-Hdelta+...delta+H-C bond path (an interaction termed hydrogen-hydrogen or H- H bonding to distinguish it from dihydrogen bonding from which it is qualitatively distinct). In addition to the intramolecular H-H interaction, a number of intermolecular interactions are shown to be involved in the packing of this molecule in the crystalline state. The effect of the nonplanarity of the molecule on the local aromaticity of each ring is also discussed.

Computational Study of the Interaction between TIBO Inhibitors and Y181 (C181), K101, and Y188 Amino Acids

The non-nucleoside inhibitors of HIV-1 reverse transcriptase (NNRTIs) are an important class of drugs employed in anti-HIV chemotherapy. TIBO compounds, which belong to the NNRTIs class, are potent inhibitors of the HIV-1 reverse transcriptase enzyme (HIV-1 RT). However, mutations in the amino acids present in the active site of these inhibitors limit their clinical use. In this work, the intermolecular interactions taking place between compounds of the TIBO family and Y181 (C181), K101, and Y188 amino acids are investigated. For this purpose the coordinates of three RT crystalline structures complexed with TIBO were taken from PDB database, and were analyzed by means of the B3LYP/6-31+G(d,p) model. The natural bond orbital (NBO) and atoms in molecules (AIM) methods indicate that not only does the Y181C mutation lead to loss of favorable interactions between the TIBO side chains and tyrosine, but it also affects the interaction between the inhibitor and K101 and Y188. Results also revealed that the interaction between TIBO and K101 is stabilized by N-H...O and N-H...S hydrogen bonds. This is the first time that the presence of the latter hydrogen bond (N-H...S) is reported to play an important role in the stabilization of the interaction between TIBO and K101. In addition the NBO and natural population analyses (NPA) indicate that the 8 Cl-TIBO inhibitor presents a more effective interaction with the Y181, K101, and Y188 than that of 9 Cl-TIBO.